ArticlePloS one2013
An extensive evaluation of read trimming effects on Illumina NGS data analysis.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 218 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
218 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis.International journal of molecular sciences · 2020Pooled it
- Unveiling the genetic blueprint of verbascoside biosynthesis inHorticulture research · 2026Article
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome.Briefings in bioinformatics · 2026Article
- Read-mapping signatures for molecular characterization of transgenic DNA insertions in paired-end Illumina data.BMC biotechnology · 2026Article
- Arbuscular mycorrhizal symbiosis in tomato roots with a diverse range of carotene accumulation.Mycorrhiza · 2026Article
- Transcriptomic analysis of zonula occludens-1 (ZO-1) knockout in ovarian cancer cell lines.Genes & genomics · 2026Article
- Overdominance for fitness: a genomic comparison between empirical and simulated data with Drosophila melanogaster.Genetics · 2026Article
- The FORGENIUS Genomic Resources: New Genotyping Tools and Genomic Data for 23 Forest Tree Species and Their Genetic Conservation Units.Molecular ecology resources · 2026Article
- Article
- Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples.BMC bioinformatics · 2026Article
- Overexpression of the maize 9-lipoxygenase gene LOX4 confers resistance to Fusarium verticillioides via the oxylipin- and jasmonic acid-mediated pathways.Journal of experimental botany · 2026Article
- Neonatal microglia replacement in mice modulates seizure severity in adulthood.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- A Test of the Long-Term Efficiency of Genetic Rescue With Drosophila melanogaster.Molecular ecology · 2025Article
- Article
- Mycorrhization and chemical seed priming boost tomato stress tolerance by changing primary and defence metabolic pathways.Journal of experimental botany · 2025Article
- PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.Current issues in molecular biology · 2025Article
- Genetic diversity and fine-scale spatial genetic structure of European beech populations along an elevational gradient.Heredity · 2025Article
- Phylogenetic comparative analysis of functional morphology sheds light on the evolution of seasonal migration in nightingale-thrushes (Turdidae: Catharus).Scientific reports · 2025Article
- A loss-of-function of ZmWRKY125 induced by CRISPR/Cas9 improves resistance against Fusarium verticillioides in maize kernels.Plant cell reports · 2025Article
158 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.